title: A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.
abstract: BACKGROUND
  Gene transcripts specifically expressed in a particular cell type (cell-type specific gene markers) are useful for its detection and isolation from a tissue or other cell mixtures. However, finding informative marker genes can be problematic when working with a poorly characterized cell type, as markers can only be unequivocally determined once the cell type has been isolated. We propose a method that could identify marker genes of an uncharacterized cell type within a mixed cell population, provided that the proportion of the cell type of interest in the mixture can be estimated by some indirect method, such as a functional assay.
  
  
  RESULTS
  We show that cell-type specific gene markers can be identified from the global gene expression of several cell mixtures that contain the cell type of interest in a known proportion by their high correlation to the concentration of the corresponding cell type across the mixtures.
  
  
  CONCLUSIONS
  Genes detected using this high-throughput strategy would be candidate markers that may be useful in detecting or purifying a cell type from a particular biological context. We present an experimental proof-of-concept of this method using cell mixtures of various well-characterized hematopoietic cell types, and we evaluate the performance of the method in a benchmark that explores the requirements and range of validity of the approach.
authors.affiliation: Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada. cpereziratxeta@gmail.com.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.forename: Femina
authors.initials: F
authors.lastname: Kanji
authors.forename: Carmen G
authors.initials: CG
authors.lastname: Palii
authors.forename: Marjorie
authors.initials: M
authors.lastname: Brand
authors.forename: Harold
authors.initials: H
authors.lastname: Atkins
authors.forename: Carol
authors.initials: C
authors.lastname: Perez-Iratxeta
mesh_terms: D045744:Cell Line, Tumor; D015870:Gene Expression; D005819:Genetic Markers; D018922:HL-60 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D019169:Jurkat Cells; D020014:K562 Cells; D059467:Transcriptome
chemical_list: D005819:Genetic Markers